The importance of microalgae as a potential source of biofuel and value-added products has led to the development of microalgae-based biorefinery in recent years. However, the downstream process including lipid extraction and the refining process remains one of the main problems for commercialization due to its low economic feasibility induced by high usage of organic solvents and energy consumption. To solve these problems, a high shear mixer (HSM) was applied to the downstream process in this study. We first demonstrated both lipid extraction and degumming process using a bench-scale HSM with concentrated wet biomass (360 g/L) of DHA-rich oleaginous Aurantiochytrium sp. The high shear-assisted lipid extraction process was developed based on key operating parameters, the solvent to wet cell (S/W) ratio, rotational speed (rpm), and temperature. Our results revealed that 90% lipid extraction yield was achieved with the lowest energy consumption (4.83 MJ/kg) and solvent usage (5.9 ml/g dry cell) at conditions of a 2:1 (w/v) of S/W ratio and 7000 rpm at 55 degrees C for 30 min treatment. In the degumming process, the impurities were removed from the crude oil by hydrating phospholipids. As a result, highly purified degummed oil with the negligible phosphorus content (5 ppm) was obtained. These results suggest that the HSM can be applied to the downstream process to obtain highly purified lipids with low energy consumption and solvent usage, thereby dramatically improving the overall economic feasibility compared to the conventional process.